a variational approach to niche construction

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields

Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches

In the past two decades, functional Magnetic Resonance Imaging has been used to relate neuronal network activity to cognitive processing and behaviour. Recently this approach has been augmented by algorithms that allow us to infer causal links between component populations of neuronal networks. Multiple inference procedures have been proposed to approach this research question but so far, each method has limitations when it comes to establishing whole-brain connectivity patterns. In this work, we discuss eight ways to infer causality in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality, Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and Transfer Entropy. We finish with formulating some recommendations for the future directions in this area

Psychophysical identity and free energy

An approach to implementing variational Bayesian inference in biological systems is considered, under which the thermodynamic free energy of a system directly encodes its variational free energy. In the case of the brain, this assumption places constraints on the neuronal encoding of generative and recognition densities, in particular requiring a stochastic population code. The resulting relationship between thermodynamic and variational free energies is prefigured in mind-brain identity theses in philosophy and in the Gestalt hypothesis of psychophysical isomorphism.Comment: 22 pages; published as a research article on 8/5/2020 in Journal of the Royal Society Interfac

Can biological quantum networks solve NP-hard problems?

There is a widespread view that the human brain is so complex that it cannot be efficiently simulated by universal Turing machines. During the last decades the question has therefore been raised whether we need to consider quantum effects to explain the imagined cognitive power of a conscious mind. This paper presents a personal view of several fields of philosophy and computational neurobiology in an attempt to suggest a realistic picture of how the brain might work as a basis for perception, consciousness and cognition. The purpose is to be able to identify and evaluate instances where quantum effects might play a significant role in cognitive processes. Not surprisingly, the conclusion is that quantum-enhanced cognition and intelligence are very unlikely to be found in biological brains. Quantum effects may certainly influence the functionality of various components and signalling pathways at the molecular level in the brain network, like ion ports, synapses, sensors, and enzymes. This might evidently influence the functionality of some nodes and perhaps even the overall intelligence of the brain network, but hardly give it any dramatically enhanced functionality. So, the conclusion is that biological quantum networks can only approximately solve small instances of NP-hard problems. On the other hand, artificial intelligence and machine learning implemented in complex dynamical systems based on genuine quantum networks can certainly be expected to show enhanced performance and quantum advantage compared with classical networks. Nevertheless, even quantum networks can only be expected to efficiently solve NP-hard problems approximately. In the end it is a question of precision - Nature is approximate.Comment: 38 page

Active inference, evidence accumulation, and the urn task

Deciding how much evidence to accumulate before making a decision is a problem we and other animals often face, but one that is not completely understood. This issue is particularly important because a tendency to sample less information (often known as reflection impulsivity) is a feature in several psychopathologies, such as psychosis. A formal understanding of information sampling may therefore clarify the computational anatomy of psychopathology. In this theoretical letter, we consider evidence accumulation in terms of active (Bayesian) inference using a generic model of Markov decision processes. Here, agents are equipped with beliefs about their own behavior--in this case, that they will make informed decisions. Normative decision making is then modeled using variational Bayes to minimize surprise about choice outcomes. Under this scheme, different facets of belief updating map naturally onto the functional anatomy of the brain (at least at a heuristic level). Of particular interest is the key role played by the expected precision of beliefs about control, which we have previously suggested may be encoded by dopaminergic neurons in the midbrain. We show that manipulating expected precision strongly affects how much information an agent characteristically samples, and thus provides a possible link between impulsivity and dopaminergic dysfunction. Our study therefore represents a step toward understanding evidence accumulation in terms of neurobiologically plausible Bayesian inference and may cast light on why this process is disordered in psychopathology

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u